Situation Report

Sector Status


COVID-19 cases (as of 17 October)


  • Kenya has reported a spike in COVID-19 infections, including among health- careworkers, since 12 March, when the first case was reported. As of 7 September, a total of 35,205 cases had been confirmed, with 599 deaths, case fatality rate (CFR) of 1.7 per cent. Nairobi city and Mombasa Counties have the highest attack rates of COVID-19 at 450.3 and 205.5 per 100,000 population respectively, compared to the national average 74 and need enhanced interventions. The total number of recoveries and discharges for COVID-19 was 20,644 as of 4 September 2020.

  • MoH attributes the high rate of infection among private health facility health-care workers (HCWs) to inadequate adherence to infection prevention and control (IPC) guidelines and inadequate supply of personal protective equipment (PPEs). Risk communication, delayed laboratory testing, and lack of contact tracing or reporting are some of the key challenges impacting needs in the COVID-19 response.

  • Health institutions have reported insufficient medical facilities including, personal protection kits for frontline health workers and community health workers, laboratory testing kits for the mass testing of the targeted communities and high-risk groups, logistical support for the quarantine facilities, and establishment of new quarantine and Isolation centres to respond to the increasing numbers of new cases and contacts across the country.

  • Provision of referral services in the 12 counties to ensure referrals 24/7 for emergency sexual and reproductive health cases, for women and girls in COVID-19 isolation centres, quarantine centres and quarantine neighbourhoods.

  • There is need to establish testing at the port of Mombasa to ensure truck drivers are tested prior to the onset of their journey in order to reduce the need for further testing at the borders and facilitate movement of goods.

  • Health authorities have reported reduced uptake of other essential health services amid the COVID-19 pandemic, including for chronic conditions and immunizations services threatening to reverse investments made towards control of communicable diseases, including TB.

  • Measles outbreaks are still active in five counties: West Pokot, Garissa, Wajir, Tana River and Kilifi. A total of 512 cases have been reported, out of which 49 were confirmed and two deaths (CFR 0.4 per cent), according to MoH. There is need for continued sensitization of health workers on the disease and its management and treatment, and distribution of guidelines on measles disease in the health facilities. Improved outreaches visits are also needed to improve immunization coverage for the affected areas.

  • The Ministry of Health has since January 2020 reported an outbreak of visceral leishmaniasis (also known as kala-azar) in Marsabit, Garissa, Kitui and Baringo counties, where a total of 146 cases with seven deaths (CFR 5 per cent) have been recorded, as of 5 September. Health authorities have reported a stock out of visceral leishmaniasis commodities especially rapid test kits, in addition to lack of vector control chemicals and IEC materials, including standard guidelines. There are limited drugs for proper treatment coupled with inadequate knowledge and lack of guidelines and protocol for healthcare workers on case management. Lack of community awareness and knowledge about the diseases and preventive measures has also contributed to its spread.


  • Health sector partners are providing support to County Health Departments and public health teams in responding to the health challenges posed by the COVID-19 pandemic and other outbreaks, including cholera, malaria and measles reporting active transmissions across the country.

  • The Cholera outbreak have been controlled in the five affected counties as of 26 August.

  • Investigation of all COVID-19 alerts across the country by the Rapid Response Teams. Rapid response, contact tracing, case management, community mobilization for risk communication and health promotion is going on in all counties. Risk communication and community engagement is on-going to enforce hygiene and social distancing, to reduce increasing transmission.

  • A total of 306,935 cumulative tests have so far been conducted by the 32 laboratories including two mobile labs located across the country. As of 31 July, a total of 1,777 truck drivers had been tested to complement the ongoing testing by the government at Malaba and Busia border.

  • Eight Epidemiologists and five Risk Communication and Community Engagement officers deployed to support COVID-19 response in key eight most affected counties: Kilifi, Mombasa, Nairobi, Nakuru, Embu, Kisumu, and Eldoret. Garissa and the refugee camps to support critical areas of health sector coordination, laboratory testing, rapid response and contact tracing teams as well as risk communication.

  • Health sector partners are supporting MoH to roll out of the new Kenya COVID-19 Home-based Care, Community Isolation, Laboratory testing strategy and contact tracing. The MoH is rolling out the home and community-based isolation and quarantine protocols focusing on Nairobi and Mombasa and other most affected counties across the country to reduce excess loads on the current facilities considering the increasing number of cases most of whom are asymptomatic.

  • About 26,000 COVID-19 testing kits and accessories donated to MoH and supply of 119,000 sets of masks for use by the frontline health workers during management of COVID-19 patients.

  • More than 9,300 people in 15 Nairobi informal settlements were supported with integrated services including: child immunization, nutrition services, curative services, ante-natal care, family planning, COVID-19 screening among other PHC services.

  • At least 540 community health volunteers in Migori County were supported to disseminate key COVID-19 preventive messages which has led to strengthened risk communication for COVID-19 and improved community involvement in prevention and control of COVID-19.

  • Completion of capacity building for Case Management and Infection Prevention and control for public and private health facilities in 10 counties in August 2020. Over 500 participants included doctors, pharmacists, nurses, laboratory, clinical officers, surveillance and public health officers benefited from the training. This also includes capacity building for sub-county risk communication and community engagement officers in 10 counties supporting the sub counties on public health education, social distancing, hygiene promotion activities.

  • Community sensitization is ongoing, including a two-week risk communication activity led by IOM in migrant-dense urban areas in Eastleigh (Nairobi), using a public address system to disseminate appropriate COVID-19 messages, targeting 100-200 households per day.

  • Support to 22 public health facilities within Nairobi Metropolitan to conduct integrated medical outreaches. A total of 4,279 people from the 15 informal settlements within Nairobi were reached with COVID-19 life-saving interventions and efforts to maintain essential health service during integrated outreach services.

  • A total of 225 health care workers in Busia County have been trained on COVID-19 IPC, case management, surveillance and contact tracing. Following the training, COVID-19 surveillance and contact tracing coordination structures have been set-up in each sub-county which has led to better planning and follow-up of surveillance activities. Another 187 health care workers from Kajiado and Machakos counties are currently being trained on COVID-19 case management and infection prevention control, expected to contribute to quality management of COVID-19 patients.

  • A total of 66,090 people (38,995 females and 27,214 males) reached through integrated medical outreaches including: child immunization, nutrition services, curative services, ante-natal care, family planning, COVID-19 screening among other PHC services. A total of 310 Community Health Volunteers (CHVs) were sensitized on COVID-19 pandemic and key modules covered included symptoms of COVID-19, spread, referral pathways, myths & facts, and stigma reduction.

  • At least 540 community health volunteers have been trained in Migori County disseminating key COVID-19 preventive messages, which has strengthened risk communication for COVID-19 prevention at community level, improved contact tracing strategies, developed structures for COVID 19 follow up at the community level, enhanced awareness of county home-based care protocol and improved community involvement in prevention and control of COVID-19.

  • Some 1.2 million people have been reached so far with information on sexual reproductive health through various media outlets including social media, webinars and print and electronic media. This included 79,350 adolescents and youth with integrated SRHR information by way of film disseminated through various social media platforms.

  • Delivered 500,000 vials of injectable contraceptives (im. DMPA) to KEMSA to be distributed to health facilities across the 47 counties.

  • A team from the Ministry of Health supported both Marsabit and Wajir counties to carry out field investigations for visceral leishmaniasis, while the national government has provided technical guidelines and fact sheets. The county health departments are undertaking enhanced surveillance activities, detection, confirmation and managing of cases and community awareness and sensitization.


  • Stigma and discrimination against people who have been discharged from quarantine and isolation centres, as well as health workers, are emerging hindering case identification and reporting.

  • Inadequate resources for operations at the sub-national level for COVID-19 surveillance activities, this is glaring at the sub-county level.

  • The long turnaround time for reliable laboratory results to clients in most counties is causing delay in public health action.

  • Uptake of other essential health services have drastically reduced since the COVID-19 pandemic. Key sectors affected are immunization, reproductive health and non-communicable diseases.

  • Complacency by community despite established community transmission now a threat to prevention.

  • Commodity insecurity at the sub-national level of personal protective equipment.

  • Low uptake of integrated digital data management systems especially for the digital case investigation form in the CHT and Kenya EMR.

  • Re-emergence of long queues of truck drivers along the major border points of entry and exit with neighbouring countries due to delays occasioned by retesting by Ugandan authorities.